The Scent Seedling is a required quest item featured in Oracle of Ages.
When Link first arrives on Crescent Island, the Tokay will come and steal all of his items. When trying to recover all of his goodies, Link will find the Wild Tokay mini-game, located at the east end of Crescent Island in the Past. The Scent Seedling serves as the prize when Link first plays the mini-game. The game operator will try to bait you into playing, by telling you the Scent Seedling is the prize. Link will need to lift up Tasty Meat and toss it at the moving Tokay on the left and right sides of the screen.
The Scent Seedling can be planted at the north end of Crescent Island within the Tree Nursery. The nearby Tokay will mention that it will take a very long time before this seed becomes a tree, and he hints that Link should come back after a long, long time. Link should then use the Harp of Ages and return to the same location in the Present. When Links arrives back at the location in the present, he'll find that Seedling has blossomed until a full blown Mystical Tree that is holding Scent Seeds.
Scent Seedling sprouting into a Mystical Tree